Stargate Atlantis: S7--A Terrible Beauty
by the morrighan
Summary: Story 2 of 5 where the adventure continues and the war commences, but will the alliances hold?
1. Chapter 1

Stargate Atlantis: S7—A Terrible Beauty

Pride.

It filled Colonel John Sheppard as he strode along the deck of the spaceship. His motions were more of a swagger, and his chest was puffed out with both satisfaction and smugness. He had been aboard spaceships many times, and even an Ancient ship or two, but this was different.

This was his ship.

He was in command of this ship instead of being just a passenger on the Daedalus or the Orion, just a lackey to the man in charge. This was his command and this baby was all his. Well, it belonged to Atlantis, of course but it was still his, under his authority and repaired and enhanced under his exacting specifications.

And Doctor Rodney McKay's, of course.

Still, he was in charge, and John could not help the feeling of hubris inflating his ego and his every step as he took in the full extent of this vessel. It was an Ancient warship, rescued from the void between the galaxies and hauled back to be placed into service once more. It was called the _Tria _but John was considering changing the name.

"Excelsior!"

John scowled and turned to see Rodney strolling towards him. If the physicist could ever be described as being radiant this would be the moment. Rodney was positively beaming as he grinned and swung his data pad under one arm like a bouquet of flowers. Confidence imbued his every step. "What?"

"Excelsior! The new name of the ship! I've decided. She's incredible, John!"

"No."

"She's incredible," Rodney continued, ignoring the ire of his friend. "We've got her powered with ZPMs and a state of the art hyperdrive, plus some Asgard technology that was a little touch and go at first but I got it working, of course! She's got a full arsenal of Drones and a Chair and missiles plus she can disengage sections if they get damaged but they better not get damaged considering all of the work I put into her!"

"Rodney!" John scolded, finally able to get a word in as the voluble scientist took a breath. John smiled. He could not be angry, not really. The ship was a marvel and both men knew it. As they both knew that this ship was their only hope against the Fugly fleet. "I told you, we can discuss names later, all right? Beaming technology?"

"Um…"

"Um?" John frowned again. He placed his hands on his hips.

Rodney shrugged. His data pad came to a halt at his side. "We're having some problems in that area. Look, it's a wonder she can fly at all! Let alone be able to take on the Fuglies and travel through hyperspace! I've taken the equivalent of a Volkswagen that was in a wreck and turned her into a Jaguar! No, into a Corvette! No...into a…anyway, you get the picture!"

"A classic Mustang and yes I get the picture. Shielding?"

"At one hundred percent now…and should hold."

"Should?" The ire was back in a flash.

Rodney merely shrugged. "Should. Look, she's untested, right? So it's about time we took her out on test drive, er, fly. I can't wait to—"

"You will have to wait." John began to walk along the deck again, heading for the command center. "We've discussed this, Rodney."

"No, Woolsey and you discussed this, not me!" Rodney followed after his friend. "John! I can at least be aboard for the test flight!"

"You've been aboard her for months fixing her up!"

"That's not the same thing as taking her out for a test fly! I should be here in case something goes wrong! Not that anything will go wrong but if for some unforeseeable reason it does you will need me here to fix it!"

"No. I'm taking her out for the meeting with Todd, and then I am swinging by Echo Base for all updated intel before venturing to the Fugly twenty and assessing the situation myself. From there we will be going directly into battle."

"You…oh. I…oh."

John paused, raising a brow as he turned to meet the gaze of his friend. "Excuse me?"

Rodney merely smiled. "I see."

John grunted a response as they reached the bridge. Both men paused, surveying the pristine consoles. The quiet hum of the engines purred under their feet. The air was cool, slightly stale but circulating. Colored lights blinked. The viewport beckoned. Its curved expanse gave a striking view of the vastness of space in which they were orbiting. Far, far below a blue green planet glinted. On that planet Atlantis floated.

She was a tiny dot amid the sapphire ocean. It was a gray city of elegant spires and power that spread out like the petals of a flower. It was a marvel and a nightmare and a spaceship all in one. It held the lives of the entire expedition team and their allies and friends.

It was home.

John nodded to the airpersons manning their stations. He slid into the command chair and rested his hands on the controls on each armrest. The ship seemed to respond to him, rumbling softly like a big cat. John smiled and let his fingers play along the armrests before he noticed Rodney watching him. "What?"

Rodney shook his head, amused. "Nothing. So…this meeting with Todd. Expecting trouble?"

"Always, but not this time. The weapons are online?"

"Of course. John," Rodney paused, growing serious, "you know you're taking a risk, letting the Wraith see this ship."

"I know. But I believe it's the only way to convince them to commit to this battle. We can match their firepower now. It should give them confidence…and some trepidation. We can keep them on their toes so they will stay in line, for now."

"And afterwards? What if the IOA wants to get hold of it to—"

"They won't. They won't be getting their grubby hands on her." The ship seemed to purr in response and John felt a smug satisfaction. "This baby is mine er, ours and she stays right here, protecting Atlantis."

"Colonel Sheppard? Receiving transmission."

"Acknowledged." John tapped a button. "This is Sheppard."

"Sheppard, this is Ellis. We're ready to beam McKay aboard. Good luck."

"What? What does he mean beam McKay aboard? I am not going on that vessel! I am not going to be beamed onto the _Aegis_! I'd rather take a Jumper than—"

"We can't spare one, just in case. Ellis, go ahead. Thanks, Rodney."

As Rodney began an outraged rant light enfolded him and he was gone, still talking. No doubt he would materialize onto the _Aegis _still talking. The thought made John smile. "Atlantis, this is Sheppard. McKay's on the _Aegis. _We're ready to head out."

"Acknowledged," came the voice of Richard Woolsey over the com. "Good luck, colonel. We'll be waiting to hear how the meeting transpired."

"Understood. Sheppard out." John settled back, staring at the immensity of space ahead of him. The burden of responsibility and command weighed upon him and he was silent for a moment, taking it all in and accepting it. "Take us out, major. Let's give her a spin round the planet before we jump to hyperspace."

"Acknowledged, sir."

John relaxed, settling back and letting the power of the machine at his command enfold him. Much like the little Puddle Jumpers the ship would respond to his ATA gene, but these systems were much more complex and required a full crew to be fully operational. Although he was connected to the ship it was not as intimate a relationship as he had with the city.

John's fingers played across the controls for a moment, assessing as the ship smoothly flew through space, circling the planet. The long-range scanners were filling a screen with information. Everything was working.

It felt good to be in the command chair.

"All right. Set course for M6H-987."

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"…not to mention the indignity of being beamed like some piece of luggage and then transported back to the city right after I upgraded their long-range scanners! And then Ellis says not even a thank you! I can't stand the arrogance of that man! And I should be aboard the _Tria _I don't care what Sheppard says! Why do these military types think they know everything? Can you believe it? Can you?"

"Huh? Sorry, I stopped listening five minutes ago."

Rodney huffed in exasperation, causing Radek Zelena to smile. The two scientists were in the cafeteria, comparing notes over their lunch. Power output was always a concern and the two men were trying to find other ways to utilize the limited number of ZPMs running the city.

First and foremost the shield and cloak had to be powered. After that came the Stargate and then everything else. The massive drain of power would someday seriously limit the city's capabilities.

"You can go on the next voyage…providing the _Tria _survives this voyage."

"She'll survive! She better! If Sheppard so much as gets a dent in her I will strangle him!" Rodney sighed, setting down his fork. "I should be on that ship."

"Atlantis needs you right here, Rodney. Just in case."

Rodney nodded. "I know. I don't like it…but I know."

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"I know." Carson Beckett frowned, shining the light into Amelia Banks-Dex's eyes again. She squinted in protest against the invasion of brightness. The doctor lowered the light. "There's nothing wrong with your optic nerve, and all scans came back clear."

Amelia shrugged. She was sitting on a bed in the infirmary. "I guess a headache is just a headache."

"Yes, but you've been having them for three days now. That's a concern, love. I will give you more pills but we need to find the source of these headaches and not just temporarily mask the symptoms."

"I need to get to work, doctor." She swung her legs over the side of the bed. "If the scans are clear what can it be? Maybe it's just stress."

"Maybe." Carson did not sound convinced, however. He handed the major a vial of pills. "Let me run a few more tests on the blood I took. How are you feeling otherwise?"

"Otherwise, fine." She considered a moment, auburn brows furrowing. "Except…"

"Except? You can tell me anything, love, in complete confidence," Carson assured. He waited. His blue eyes were full of concern and compassion.

Amelia hesitated. She ran a hand over her tightly bound auburn hair. She was loath to talk about it. She didn't want to sound as crazy as Moira had been. "Sometimes…I feel like I'm not…well, like someone else is looking through my-"

"Amelia? Are you all right?" Ronon Dex asked, hastening towards them. The Satedan towered over his wife but she was not at all intimidated.

Amelia smiled, moving to her feet. "Of course. Just another pesky headache but Beckett has taken care of me. Let's grab some late lunch."

"Wait, wait! What did you mean by—" Carson asked, seizing upon her words.

"Nothing, doc. I'm just tired and these damn headaches make me feel woozy sometimes, you know? I'll be fine. Let's go, Ronon." She took her husband's arm and led him out of the infirmary.

Carson stared after them as suspicions formed.


	2. Chapter 2

Stargate Atlantis: S7—A Terrible Beauty2

Effortlessly the _Tria _burst out of the hyperspace window and smoothly transitioned to real space. John smiled and moved to his feet. He stared out the viewport at the planet amid the darkness and the stars. It was a white ball that was growing larger and larger as they approached. It was a frozen world without a Stargate. It had once been the secret location of an Ancient lab, and more recently the hideout of the rebel Asgard.

Now it was a wasteland.

The buildings were derelict, having been mostly destroyed in the successful attempt to obliterate the dangerous Attero device. Now the planet was void of life of any kind. It was isolated. It was forgotten. It was alone.

It was the perfect place for a secret meeting, or an ambush.

"Status?" John barked, circling round the bridge like a hawk looking for prey.

"No energy readings of any kind, sir. We seem to be the first ones here."

"Very good, major. Edwards, you have the helm while I am gone." John tapped his earpiece. "Team Foxtrot to the Jumper bay. Sheppard out."

"Detecting hyperspace window, sir!"

"Ah…our guests have arrived. Once they are clear transmit the coordinates. We'll be waiting for them." With a last smug glance at the bridge John sprinted to the Jumper bay. He wanted to reach the planet's surface before the Wraith did and keep the Jumper cloaked. There was no need to reveal that as yet the _Tria _was lacking beaming technology.

As far as John could tell it was ship's only weakness.

With practiced ease John flew the Jumper to the planet and landed near the abandoned lab. He led the men through the frozen waves of snow towards the dilapidated buildings. The air was cold, but manageable. Ice and frost crunched under the men's boots. In their black uniforms they stood out for a mile. John raised his hand and the group halted.

A beam of light descended from the sky. Lilac tones shaded the white snow then faded to reveal a group of Wraith warriors. Instantly the men's weapons lifted and were aimed. The Wraith responded in kind.

A few tense seconded passed.

Todd stepped out of the phalanx of warriors, open hands spread out to either side. "John Sheppard."

John scowled. He advanced, lowering his weapon reluctantly. "I told you to come alone."

"And so I have. One ship only. You really did not expect me to travel here by myself, did you?"

John grumbled a reply. "Let's talk inside. This way." He turned, glanced at his men. The look was enough to convey his orders. The men slowly lowered their weapons but kept their gazes locked on the Wraith. The Wraith lowered their weapons, silent.

Todd's chuckle was the only sound in the cold, cold air as he followed after John.

John stepped over and around the debris. It was just as cold inside the facility but it was somewhat protected from the snow and ice. He brushed off a toppled table and righted it. His touch made the console hum for a moment. He set down a laptop and opened it, typing codes with his chilly fingers. "All the intel you need is right here. Position, deployment, approximation of enemy numbers and projections of their course. More importantly you need to be at these coordinates in a week. We'll do the same, and converge upon them at this point." John watched the graphics as they came to life, illustrating his words. He straightened, turning suddenly. "What?" he snapped.

Todd was eying John speculatively, head tilted to one side. "You have an Ancient warship."

John smiled. "Yeah. Oh…did I fail to mention that?"

"This changes things considerably."

"Indeed it does, pal. Lucky for you right now we are on the same side. Let's get down to brass tacks. How many ships are you bringing to this fight?" John folded his arms across his chest, waiting.

Todd's eyes narrowed. "Our queen has decided that we shall commit four Hive ships to this enterprise."

"Four? We need more than that, buddy! You've got a whole damn fleet at your fingertips! We need half of that, at least, plus what we're bringing to the fight, plus our allies! Haven't you seen the numbers?" John glanced at the laptop and its display.

"Indeed I have, John Sheppard, but the queen's decision is final. She will not risk the entire fleet on a fool's errand."

"A fool's errand? I see." John glared at the Wraith. "If we don't kick these guys out now we may never get the chance again. You do see that, right? You need to tell your queen that this is our one and only shot at this."

"Our queen is aware of this, John Sheppard."

"Then you…hang on." John tapped his earpiece as it squawked. "What?"

"Another Hive ship has just arrived, sir, and is heading for us. Orders?"

"Shit. Shields at maximum." John eyed Todd. "I told you to come alone, damn it! Why is there another ship here?"

Todd shrugged. "I have no idea. Our queen must have decided that you might need more…persuading." Todd's smile was more chilling than the air.

John smiled. "Edwards…prepare to take it out."

"Sir?"

"You heard me. On my mark destroy it."

"What are you doing, John Sheppard?" Todd stared. Surprise and anger flared in his eyes and he took a menacing step towards the human. His feeding hand flexed in response.

"I told you to come alone. You broke that agreement, and I am tired of being lied to and treated like some fucking errand boy. Besides, you need to see this ship of ours is operational. And if you step out of line again I won't hesitate to use it."

"If you fire upon that second ship they will respond in kind, and so will mine."

"Then you better get back up there and make sure your ship doesn't join the fray. Take this." John snatched the laptop and shoved it into Todd's hands. They hastened out of the building and towards the tense stand-off of their parties.

Todd moved to the Wraith, speaking into a communicator on his wrist. He looked over at John. "I have tried to communicate with the other ship but they are jamming my signal. It could be a rival Hive…but I find that impossible."

"Anything's possible."

"If you give me time to try to contact them to—"

"You got five minutes." John tapped his earpiece, eying the sky. "Edwards, power up those missiles."

"You are bluffing!" Todd snarled, about to lunge forward. The Wraith aimed their weapons. Power sizzled in the cold air. The marines aimed their P90s but John stood, almost nonchalant as he kept watching the pale blue sky. "Rescind that order!"

"No. You better get back to your ship, Todd. Clock's ticking." John pointed at the laptop. "Be at those coordinates in a week. And next time…stick to our agreement."

Todd was formulating a reply when a beam of light cascaded down and removed the Wraith from sight.

"Let's move!" John and the men raced back to the Jumper. John quickly piloted the ship to the safety of the _Tria. _Once the docking bay was secure he sprinted to the command bridge and moved to the viewport. He ignored the snow dripping from his boots. "Status?"

"There's some chatter between the two ships now, sir. No overt hostile movement from either one, but the second one is powering weapons. It could be a ruse."

"Target the interloper."

"Sir?"

"You heard. If we don't show a strong hand now they will think they can roll over us later." John folded his arms across his chest. "Ready the missiles and target the most vulnerable areas. Let's see what this baby can do," he muttered softly. He knew he was being rash, reckless. Nevertheless the decision felt right and John always trusted his gut feelings.

He couldn't wait to see the ship in action, and power she possessed.

"Incoming transmission!"

"Put it on speaker."

"John Sheppard! If you fire upon the second vessel we will consider it an act of war."

"It already is an act of war since you broke our agreement. Don't you think I don't know what you're doing? You thought to find us outgunned. Well, you thought wrong. You tell that ship to stand down now or I will destroy it!"

"This was none of my doing, John Sheppard. They say they have orders to take you to our queen." The surprise in Todd's voice was evident.

"Really? Now isn't that interesting? I actually believe you for once, Todd. You better get clear. Our deal stands." John moved to sit in the command chair. His fingers stroked the controls, waiting, waiting. He watched as one Hive ship drew away and the other one grew nearer, nearer.

"Sir? Power levels are increasing. I am detecting a surge…like a tractor beam."

"Sonuvabitch. Fire missiles four, five and six now. Now!"

The ship seemed to hum and jolt as missiles flew from it. At the same time the Hive abruptly began to fire. John tensed as the ship maneuvered, but the lasers bounced harmlessly off the shielding as it was restored. Harmless bursts of pink light bounced along the viewport.

There was a sudden brilliant flash of light as a tremendous explosion catapulted the Hive ship in a death spiral. The ship shattered, breaking into shards as it was ripped through and through. John squinted even as the viewport darkened against the tide of light assaulting it.

Huge pieces of wreckage were catapulted through space. Many would land on the frozen planet beneath them unless they burned up in the atmosphere. Unmanned darts scattered like petals on the wind, as did the lifeless bodies of countless Wraith.

There was silence on deck as the bright light of the explosion slowly, slowly faded. The stars came back into view. It felt like the crew was holding its collective breath. None dared gainsay the military commander's decisions.

John could feel the ship like a living thing. It was as if he had unleashed a wildcat onto unsuspecting prey, and now had to reign it back in before it could do more damage. All of that lethal power was under his control, and now he understood the underlying arrogance of such men as Caldwell and Ellis. Even of the Ancients before they had been defeated by the Wraith.

It was as heady as a drug, and as dangerous.

"Input the coordinates for Echo Base," John finally spoke and the spell was broken. Normalcy was restored. "Status of Todd's ship?"

"It entered a hyperspace window, sir, before the attack."

"Good. Good." John relaxed into the chair, thoughtful and confident.

The Wraith would not dare to underestimate him again.


	3. Chapter 3

Stargate Atlantis: S7—A Terrible Beauty3

Echo Base was a hub of activity. Scientists were moving from console to console, taking into radios and to each other. Data pads were everywhere and the constant stream of information and equations was dizzying.

It was bitterly cold. John still had a chill from the short walk from the Stargate to the bunker. The _Tria _was in orbit around the neighboring planet, ostensibly hidden from any prying eyes. John had taken a Jumper and parked it near the Stargate. He couldn't help but be overly cautious. If the Ancient warship was his trump card this base and the personnel on it were his ace in the hole.

Snow still clung to his coat and to his boots as he stomped towards the control room, leaving a trail of melting puddles in his wake. The planet was like a giant snowball. Nearly all of its surface was covered in snow, locked in a permanent Ice Age. Initially a science team had been sent here to study the environment. When life had been found the excitement had grown.

At his approach the scientists stared, falling silent for an assessing moment. Then they resumed their work and their arguments.

"Status?" John asked abruptly.

The man in charge turned, startled. He was short and squat, with a red mustache and beard. He reminded John of a badger, and the man was just as tenacious. Chris Sands was a scientist first and foremost, but he knew the importance of monitoring all activity of the enemy fleet. "Colonel Sheppard! We've sent the latest updates to Atlantis."

"I know. I wanted to see them personally. How's progress on the language decryption?"

"It's an ongoing work in progress, but we're making strides every day," Chris hastily assured. "Here is the latest monitoring of the Fugly position. As you can see they haven't moved from their latest course. They seem to be waiting for something. Radio chatter's been frequent and given us quite a boon for the translation program."

John glanced at the proffered data pad. "Give me everything you have. I'll be back in thirty. I want to check on Green's progress myself."

Before the other man could reply John was gone.

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"…and I need an update on their biological development too! And you better hurry because he wants that translation program yesterday!"

John smiled at the voice over the com as he entered a lab. He paused. There was a woman working alone. Her back was towards him as she sat at a computer.

"Tell Sheppard to keep his pants on! It will be ready when it's ready!"

John drawled, "Actually I was hoping to take off my pants…or better yet have you do it, Green. Just don't tell my wife because she'll get pissed."

"John!" The woman jumped out of her chair, startled. She smiled and rushed to the military commander, engulfing him in a hug. "Oh John! John, I've missed you!"

"Moira," John said. He hugged her tightly, only drawing back to catch her mouth in several kisses. Each was more passionate than the last and suddenly Moira found herself pressed against the desk.

"John!" she scolded, catching her breath. She touched his face gently, worry filling her brown eyes. "You want the translation program."

"Among other things, yes, baby."

"You look tired."

"Yeah, I am. It…it hasn't been easy," he admitted. He lowered his gaze for a moment, loath to reveal his troubles to her. She knew them all the same.

"John." She kissed him, then slid free of his embrace to move to the computer. "I was afraid this would happen. You can tell them, you know. You don't have to continue the charade."

He followed after her. "No. It's safer this way, at least until this threat is eliminated. You have to trust me, Moira."

"Of course, John. Here." She turned and held out a flash drive, but suddenly snatched it back before he could take it. "This program is evolving, but it won't be able to translate everything. It is learning as it goes, as we learn. John, I need to come with you on this."

"No."

"Hear me out. I will be better able to translate their language than this device. Whatever is in here," she touched her brow, "can translate better than the computer. Especially after the aphasia. You remember, right?"

John nodded, recalling it all too well…

_John sits at the hospital bed, staring at his newlywed wife. Scans had revealed nothing but a swelling that was being treated. Nevertheless John sits, vigilant. When Moira stirs he takes her hand into his. "Moira? Can you hear me? Doctor!" he shouts over his shoulder._

"_I can hear you fine, sweetie," Moira says, blinking at him. She struggles to sit up in the bed. "Where am I? What happened? Oh! The car! Are you all right, John?"_

_John meets her gaze. "I'm fine, baby, don't you worry. You took the fall. Doc?"_

"_It was so…maybe it would have been better if they all thought I was dead…" she mutters, and John's gaze narrows, about to refute what she has said._

"_Let me see how she's doing. Moira, what can you remember?"_

"_I remember the car and the…" The rest comes out in an unintelligible language. The doctor nearly drops his penlight as the strange, guttural sounds issue from Moira's mouth. _

"_What the…what language is that? I've never heard anything like that in my life!"_

"_I have," John grimly says. He recognizes that what sounds like gibberish is in fact the spoken language of the Fuglies._

"You will need real time communications, right?" Moira continued, jolting John out of the memory. "I have recorded as much as I can remember, and with constant access to their language I may be able to translate more! I have to be with you on this mission."

"And I said no."

"John! Stop being so pigheaded and—"

John snatched the device from Moira and placed it into this pocket. "I don't have time to argue about this, all right? You are staying right here, Moy, as we agreed. When this is all over I will come for you."

"John! You will need me on the—"

"I need you safe, Moira! All right? Now let's talk about something else because you know what arguing with you does to me!" He sounded furious, but the gruff edge to his voice revealed another emotion.

Moira glared at him, hands on her hips. It was difficult to be too angry with him. When John was angry he was incredibly sexy. "Fine! We've been making some startling progress in identifying the genetic factors. The methylation pattern could explain their bone density as well as the environment, of course and the RNA strands to-"

"Never mind!" John raised a hand, forestalling her. "I don't want to hear that now! I want…WHAT?" he snarled as a voice pinged in his ear. "Oh…okay. Shit."

"John?" Moira stood, staring at him. "You have to leave, don't you?"

"Afraid so, baby." John sighed, shrugged. "I promise I'll have more time next time. Thanks for this, Moy." He patted his pocket where the flash drive resided.

"It would be better if I went with you…John wait!"

John was heading for the door. He halted. "It's better this way, Moira. You know that." It was always difficult to leave her, yet leave her he must, for the time being.

"I can't let you leave my lab like that."

"Like what?" He turned, puzzled at her serious tone.

Moira smiled at him. She stepped to him, invitation obvious. "Colonel Sheppard, it would be very remiss of me to let you leave with this, now wouldn't it?" She touched his chest and slid her hand down to scrape her fingernails along his growing erection.

John groaned in response. "Um…well, you know arguing with you always does that to me."

Moira kissed him. "Yes, sweetie. I can't let you leave with that, now can I? So…deployment in five?" She stepped back from him, flirtatiously tilting her head.

John licked his lips. He smiled. He just smiled.

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"Colonel Sheppard, copy? Where the devil is the man?" Chris fumed, shaking his head.

"I'm right here. I was busy…consulting…with Green. Deeply consulting," he boasted. John sauntered into the control room, fighting to keep the smug smile off his face. Pleasure still echoed along his body. The sex had been quick, hot, and a little rough but extremely satisfying for both parties. John licked his lips and glanced at the console. "The _Tria_?" he guessed.

"Yes. There's an urgent transmission for—"

John stepped past the man and tapped the console. "This is Sheppard." He swallowed. His voice still sounded raspy and he allowed a smirk to cross his face. His lower, gruff tones were always a turn-on for Moira. "Report."

"Colonel Sheppard? Long-range scanners are detecting energy fluctuations and—"

"The fleet's on the move again!" shouted a technician at the same time. "Projecting real time directions…sir?"

"Put it on the board! Edwards, are you getting this?" John moved to view the screen. The red dots representing the Fugly fleet were moving en masse. "Where are they headed? Are they opening a hyperspace window?"

"Negative, sir, no wormholes yet," Edwards answered from the ship.

"The next quadrant….they look like they are heading for a group of planets."

"ETA?" John asked, scowling. He rested his hands on his hips, leaning slightly to watch the display.

"At the rate of speed and the distance to that planetary system and assuming that the variables don't change—"

"Just give me a damn timetable!"

"One week, give or take," the technician answered quickly.

John inwardly swore. Hearing a snort he straightened, whirling with a deadly glare. Moira was standing at the threshold, ogling him. She smiled. John smiled, gaze narrowing in reprimand. He turned back to the screen. "Keep tracking them. I want you to post updates to Atlantis every hour! Edwards, I'll be en route momentarily. Transmit our situation to Atlantis." He turned and strode towards Moira. "Green, a word."

"Of course, colonel." Moira quickly followed him as they walked down the hallway. She caught his arm. "John—"

John turned and pulled her into a lengthy kiss. He freed her. "I gotta go, baby. Damn Fuglies have moved up my timetable and—"

"Homo erectus and if they are heading for a planet that could mean—"

"—I gotta get our allies moving quicker than I thought and make damn sure the Wraith are there or this engagement will be short-lived, wait, mean what?"

"What?"

"What do you think that means? The planet? Colonization?"

"Or destruction. John…John…be careful!" She hugged him suddenly.

John held her close. "Don't you worry, Moira. I'll be fine. I've got the best ship out here now."

"John…if it will make it easier for you then tell them. Tell them about me. I am safe here so you can tell them now if it will make—"

"No, not yet. Something's not right, Moira, and until it is you are safer this way, as we agreed." He ran his fingers up and down her arm. "After this you and I are finally going to go on that honeymoon, all right?"

"Okay, John. Although I would be perfectly happy here with you. You wouldn't believe what we discovered! There are mammoths here! Actual living mammoths, John! We have an unprecedented opportunity to—"

"Whoa on the science talk!" he joked, smiling. "You can tell me all about them later."

"Oh I will!" She laughed at his mock groan, but grew somber. "John."

He kissed her. "Back ASAP, baby, that's a promise. Now get that pert little ass back to your lab and get to work!"

"Yes, sir!" She kissed him again. "John…"

"I know. I gotta go." Before she could detain him he left the base.

Moira sighed, standing alone in the hallway.

There was so much to tell him and so little time.


	4. Chapter 4

Stargate Atlantis: S7—A Terrible Beauty4

"Status!" John barked. He settled into the command chair of the _Tria _even as the ship was heading away from the ice planet.

"Tracking them now, sir. They are moving but at sublight. They're not in any hurry."

"Good. Plot a parallel course out of scanner range. Time we took a look at them. Anders, find everything you can about the planets in their trajectory. We need to know what's out there." John settled back and let his fingers play over the armrests, much as he had let them play over Moira's body. He smiled at the memory but pushed it aside. Now was not the time to dwell on erotic pursuits.

A spray of light convulsed and the ship shot into the wormhole. Streams of blue flight filled the viewport. The ship rumbled like a contented big cat, making the long journey in easy strides.

John sat forward and pulled the translation flash drive from his pocket. He slotted it into this data pad and then into the control pad. "Re-route all radio transmissions to me here."

"Sir?"

John smiled at the baffled technician. "I've got an app for that now. Never mind," he added to the technician's even more puzzled expression.

"Bringing up the intel on the planets, sir. There's not much but they are inhabited."

"Shit," John whispered. He scanned the data. They were the usual agrarian communities, victimized by the Wraith for centuries and unable to develop any significant technology. Way out here even the Ancients seemed to have abandoned them. There were no records of any Ancient cities or laboratories. "Gate access?"

"Yes, sir."

"But there probably wouldn't be time to evacuate," John mused, rubbing his chin. "Better we stop them before they get there."

The ship dropped out of hyperspace.

"Crap," John muttered, and his word echoed the alarmed sentiments of the crew.

The Fugly ships were large. Even at this distance they appeared immense, like floating islands in the sea of darkness that was space. As the scans collected data and began counting the fleet John could feel his confidence flagging. He scowled, reading the information and quickly adjusting his own calculations. Even with an Ancient Warship at his disposal, plus some Wraith Hive ships and whatever his other allies could bring to bear this was going to be an uphill battle.

"Get us closer but keep us out of scanner range. Decker, any radio transmissions?"

"Too sporadic, sir."

"Keep trying on all frequencies and patch it through to me." John sat forward, hands clasping the armrests of the command chair. Even with the compliment of Darts and Jumpers and F-302s plus other smaller fighters the Fugly vessels probably contained far more ships if it came to that kind of combat. It would be one hell of a dogfight in any case.

"Circle round but keep out of scanner range," he ordered. He studied the formation of the large vessels, noting the strange mark on each one. John considered sending out some cloaked Jumpers to get a better look but decided against it. It was too risky and he didn't want to tip his hand prematurely.

He glanced at the translation program. Words were popping up on the screen, interspersed among sentences of gibberish. So far nothing made sense. John looked over at another screen. The numbers were not encouraging.

"Colonel Sheppard, I'm detecting another hyperspace window! It's parallel to our course."

"Great. Now who's joining the party?"

A blur of stars yawned and lilac light folded, revealing a Wraith cruiser. The ship flew into space.

"We're being hailed."

"Maintain radio silence."

"It's the Wraith, sir."

"I realize that, Jenkins. Maintain radio silence. Fugly status?"

"We haven't been detected yet, sir."

"Let's keep it that way. If they wanna follow us into the lion's den they are on their own. What the hell are they doing out here? Probably reconnaissance the same as us," he realized, answering his own question.

The Wraith cruiser changed trajectory, moving perilously closer to the Fugly fleet. John's fingers moved on the controls, maximizing the image. There was a blur of motion as shields were raised, but not before a swarm of single fighters flew out of one of the Fugly vessels. They flew unerringly towards their goal, even as the Wraith ship glimmered with its own shield.

Something was wrong. The shield was flickering.

"I'm detecting some sort of energy field, sir, creating interference!"

"I can see that. Take us out of that trajectory. If they've got that kind of tech we are in serious trouble. Can we deploy counter measures, if need be?"

"Maybe, sir…I'm not sure."

"Great."

"We're being hailed again, sir."

"Ignore it. They're gonna give away our position! Hard to aft and give them plenty of room!"

An alarm sounded as something struck the side of the _Tria. _ Quickly the shields were raised. John stood, moving closer to the viewport. The Wraith cruiser was taking some serious damage. Explosions littered the vessel, great globs of yellow light that were silent in space. A fleet of Darts emerged to combat the fighters. Lasers crisscrossed in a frenzy of activity.

"Sir! We've got incoming. I think they are hitting us because—"

"We're in the way! Get us out of range, now!" John ordered. He moved back to his command chair, half tempted to join the fight but knowing that in this instance discretion was the better part of valor. He glanced at his data pad. More words were being translated and John read over them quickly, trying to make sentences out of the jumble.

The _Tria _swerved and shook as something else hit the shield. John looked up to see the Wraith cruiser limping out of the way, as two Fugly ships were closing in like predators. "Lower the shields."

"Sir?"

"Lower the shields. We can't let them get that ship! We need to take it out of the equation before they give the game away! The Fuglies are gonna board her! Fire missiles on my mark. Decker, plot a hyperspace window now!" John glanced down at the data pad. He settled back into the command chair, forgetting for a moment that it wasn't an Ancient Control Chair that would fire Drones. He frowned, realizing. He glanced at the data pad again. "Mark."

Twin missiles flew out of the _Tria_ and into the damaged Wraith cruiser. There was a tremendous blast of light as the ship was destroyed, along with several Darts and fighters nearby. John leaned forward as the Fugly vessels changed course, heading in his direction. Green beams of light were aiming at him.

"Shields at maximum! Get us out of here now! Evasive maneuvers!"

The ship rumbled in response. It shook as it took a hit before the shields rose, protecting it. Accelerating the ship shot through the hyperspace window and to safety.

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"Let me get this right. You encountered an unexpected second Wraith Hive ship at the meeting and destroyed it to keep the Wraith in line. Then you encountered a third Wraith cruiser and ignored their communications, instead helping the Fuglies destroy them! And you sustained damage getting away from them."

"Minimal damage," John corrected as he stood in Richard's office. His hands were clasped behind his back. "But yes, the rest is accurate."

Richard sighed, about to speak when Abraham accused, "You deliberately provoked our allies!"

John met the colonel's irate gaze, cool and collected. "No. I gave them a message that I won't tolerate any deviation from our plans and our agreements. As for the one destroyed by the Fuglies I couldn't risk revealing our position by responding to them. We were there on a strictly observational mission, nothing more."

"But now they know! They know about us!"

"No," John replied to Richard's exclamation. "They only know a Wraith cruiser wandered too close. It was destroyed before any intel could be revealed. If they realized the other ship was an Ancient vessel than perhaps they will be more cautious."

"What made you decide to destroy the Wraith ship?"

"The translation program." John addressed Abraham now. "It works. The Fuglies were not going to destroy the Wraith cruiser. They were going to board it. If any of our plans were on that ship it could have been disastrous for all of us. I stand by my decisions, sir."

"As do I." John stared, surprised by Abraham's endorsement.

"What?" Richard moved to his feet. He was shocked by the sheer callousness of the two military men. "You do realize that when word gets back to the Wraith they may terminate our alliance! And if they are not with us we don't have a chance in hell of defeating the Fuglies!"

"It's an acceptable risk, Mr. Woolsey," Abraham informed.

"Acceptable to you, perhaps, Colonel Ellis, but will it be acceptable to the Wraith?"

The question hung unanswered in the air.

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"Damn it! What did you do, dare them to fire on her? Look at this! The hull is compromised and you came this close to damaging a major system!" Rodney snapped his fingers and shoved up his visor. He was irate, glaring as he was on his knees, data pad balanced precariously near him on a protruding shelf. "Next time try using the shield before an engagement, all right? At least the missiles worked smoothly! And the scanners recorded everything so now we know the extent of their fleet. But damn it look at this! Now she's scratched!"

John shrugged and stared down at the angry physicist. "Sorry."

"Sorry? Sorry?" Rodney shut the panel and checked his data pad. "Remind me to never let your borrow anything!"

John chuckled. "If she's not battle-worthy she's no good to me, you know."

"I know. Hey…" Rodney's voice lowered and a smile appeared. "How's Moira?"

"Ssh!" John glanced round, but the two men were alone in the bowels of the ship. "Fine. More than fine, actually." John's smirk revealed all.

Rodney raised a hand. "Spare me the details. And the translation program?"

"Worked like a charm, as I knew it would." He hesitated, glancing round again. "She…she suggested I drop the charade and just…tell them."

Rodney met his friend's gaze. "And what do you think?"

"I dunno. She saw it was bothering me. She sees everything!" he complained. "But I…I don't think it is safe enough yet."

"Safe enough for whom, John? For her…or for you?"

"For the both of us, but mainly for her. I can't…I can't shake this feeling, Rodney, and until I do don't say a word, okay?"

"Okay. Now let me get back to work putting my ship together!"

John smiled. "Okay. But you mean my ship."

Rodney snorted in response.


	5. Chapter 5

Stargate Atlantis: S7—A Terrible Beauty5

John tossed and turned, tossed and turned. Frustrated he shoved down the blankets. He kicked his way out of them and sprawled onto his back. He kept his eyes shut, thinking that if he pretended to sleep it would eventually come. It wasn't the approaching battle that kept him awake. He had done everything in his power to ensure victory, and however the chips fell he knew that he would prevail, one way or another.

It was the thought of Moira that kept sleep away from him.

He tried to relax, letting his mind wander over the erotic memories; the feel of her softness and curves yielding to him; the taste of her mouth and skin; the soft sounds she made as they reached mutual satisfaction; the intimacies that he found himself craving even now. He sighed. He missed the sex of course, but it was more than that.

He missed her.

He knew the decision had been a correct one. Much as it rankled he knew he had to keep her survival a secret, at least for now. He couldn't explain how he knew she could be in danger; only that she was. The city had told him, and John never doubted the city, or his gut feelings.

It had been the same when he had told her his plan…

"_What?" Moira stands, hands on hips as she stares at her new husband. They are standing outside the SGC. It is a beautiful autumn day and the leaves are all changing into yellow. _

"_Just what you said, Moy. It would be better if everyone thought you were…um…you know. For now. Something's not right and until it is you are safer this way."_

"_You sound as paranoid as me, John. I…I don't know if I can go back to Atlantis…after…" She looks away from him. The memories of what she had endured were still vivid. They were still scars that might never go away._

_John steps closer and takes her hands into his. He fingers the wedding ring. "I know. That's why you'll be at Echo Base helping with the translation program. We've got a listening post there that is picking up all of the radio frequencies of the Fuglies."_

"_Homo erectus," she automatically corrects, causing him to smile, "and just how are you going to accomplish this, Colonel Sheppard? Will you be enlisting the help of a dead woman now?" She meets his gaze. "How will you sneak me aboard?"_

_John frees her hands. He steals a kiss before turning as a group of men approach. "Ah. We're ready to beam aboard."_

"_I'll inform the Daedalus. This must be Doctor Green?"_

"_Yes." John glances at Moira who is staring at him. "This is Doctor Green."_

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"Doctor Green?"

Moira was staring at a computer screen. She was lost in thought, lost in the memories of her new husband. She was worrying about him. Their time together had been so short, as always. They saw each other infrequently, and it was starting to wear her down. She understood the reasons, the necessity, and she didn't want to go back to Atlantis.

Still, if John could only take a week here it would mean the world to her.

"Doctor Green?"

She knew he didn't have the time. She knew that these enforced separations weighed heavily on him, as much as they did on her. Or least she thought she did. Sometimes doubts would surface. Sometimes doubts would emerge even now; even after all they had endured, even after getting married. Was John Sheppard the aloof man of her hallucinations or the passionate lover who had just made time to be with her, however briefly?

She found it hard to believe that this man, this impossibly gorgeous and complicated man loved her.

"Doctor Green!"

Startled she jolted upright and spun round in her chair. A blush suffused her features. In her rambling reminiscing she had forgotten her alias. "Yes? Sorry, I was—"

"If you have any updates on the translation program you need to send them now. The mission will begin in a few hours."

"Of course." She turned back to the computer, feeling tears fill her eyes. "Sending them now. The flashdrive I gave to Colonel Sheppard was complete but it still would have been better if I was aboard the ship with him, er them. The program can only make calculated guesses and learns as it goes."

"Colonel Sheppard was very firm about you staying here, Doctor Green. The program will run as it was devised, correct?"

"Yes, with the proper input and Gaelic transitions, it should. I mean it will." Moira hoped she sounded more confident than she actually felt.

"What was the other thing?"

"Oh! This." Moira was grateful for the change in subject to occupy her mind. "I've found an older database from when the Ancients were here. There's a lot to go through but it seems to involve the Wraith and experimentation. There were some old records in both Ancient and Wraith which I am working on translating."

"Both Ancient and Wraith? Are you suggesting they were working together?" Sands's eyebrows rose in unison.

"Possibly. We're working with them right now. Perhaps the Ancients did too, or just a rogue element. Whatever it was it seems to have involved genetic research of some kind."

"Creating the Wraith…or destroying them?"

"I'm not sure yet. The data is incomplete. This could have been under the radar, as it were, considering how distant this planet is from the rest of the galaxy. Something seems to have happened here. The records break off rather abruptly."

"Do you think this was before the planet was seeded with Ice Age life?" Chris pondered.

Moira shrugged. "Possibly, or it could have been at the same time. Whatever happened caused the base to be abandoned, that much is clear. It could prove useful for the future."

"All right. Pursue that in the meantime. And let's hope we do have a future. Let's hope for all of our sakes that this translation program works."

"It will work!" she fumed, but hearing him leave she stared at the computer. Data wavered in front of her as she blinked back the tears of worry and heartache and sorrow….

"_It will work!" John stands in his quarters on the Apollo, angrily facing her. His hands are on his hips and his scowl only accentuates his handsome features. It just wasn't fair that the angrier he became the sexier he became._

"_It won't!" Moira argues, glaring at him. "What if the real Doctor Green shows up and wonders why the hell she isn't in the Pegasus Galaxy? What if someone recognizes me? What if I slip up and inadvertently forget this new identity? What if you—"_

"_It will work!" he insists. He lowers his voice as he grasps her arms and gently pulls her closer to him. Arguing with her always gets him hard and already his lower body is raring to go. A smirk slides across his perfect lips. _

"_John!" she scolds, knowing full well what he is feeling and wanting. "I'm serious! What if this Doctor Green shows up at the SGC demanding that her—"_

"_She won't. I got it covered, all right? You are now Doctor Green."_

"_You got it covered? How? Did you bribe someone or…Rodney? Rodney did something."_

"_Yeah."_

"_But that doesn't mean this Doctor Green won't come calling to the—"_

_John kisses her, interrupting her words. He pulls her closer and stares into her eyes. "It will work. You have to trust me, Moira. Nothing is going to get in the way, all right? Nothing gets in our way. Nothing."_

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"Nothing." John sighed and ran a hand through his disordered hair. He sat in the mess hall, going over the figures and facts again on his data pad until his head started to spin. He shut the data pad and glared at it, as if the machine were the source of his bad mood.

"I think you've done everything you can for this mission. No need to worry over it. Besides, isn't that my job?"

John smiled as he met Rodney's gaze. The physicist was going over his own data pad, munching on a handful of popcorn. "Oh yeah. Right. So it is." John reached over and grabbed a handful of popcorn. "I hope we don't run out of this again."

"Me too. Think Woolsey would look the other way if we ordered a double quantity?"

"Make it a triple." The two men smiled at the jest.

"You'd think popcorn would have been invented out here, somewhere."

"They don't have microwaves."

"You can make popcorn without a microwave! Remember Jiffy Pop?"

"Oh yeah…as a kid I recall that."

Rodney met his friend's gaze. "I still think I should be aboard the _Tria_ with you, John."

"We've had this discussion, Rodney. You are more needed here."

"I know that, but I think I will be even more needed on our ship. Just listen to me," Rodney continued, raising a hand to forestall any of John's objections. "The systems are advanced. I mean really advanced, and the updates I've engineered are way beyond complicated. There's enough firepower in her to take out several of those Fugly ships but if anything goes wrong, not that it will but in case it does you will need me there to fix it! Not to mention I can continue to keep trying to integrate the beaming technology into the Ancient interface, should we need it!"

"No."

"Are you even listening to me?"

"No." Before Rodney could implode John continued, "It's a done deal, all right? You keep Atlantis safe while I go save the galaxy. All in a day's work, right?" John sighed and lowered his voice, although the two men were alone. "Look…if anything happens to me, you know…if I don't make it back…I need you to look after Moira. Make sure she's safe and gets back to Earth, okay?"

Rodney's blue eyes widened. "Of course, John, don't be ridiculous!"

"Thanks."

"Nothing's going to happen to you anyway. We got this."

"Yeah…we got this."

Silence fell as the two men resumed studying their data pads.


End file.
